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- PDB-4ptc: Structure of a carboxamide compound (3) (2-{2-[(CYCLOPROPYLCARBON... -

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Open data


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Basic information

Entry
Database: PDB / ID: 4ptc
TitleStructure of a carboxamide compound (3) (2-{2-[(CYCLOPROPYLCARBONYL)AMINO]PYRIDIN-4-YL}-4-OXO-4H-1LAMBDA~4~,3-THIAZOLE-5-CARBOXAMIDE) to GSK3b
ComponentsGlycogen synthase kinase-3 beta
Keywordstransferase/transferase inhibitor / Serine/threonine kinase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation ...neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / positive regulation of cilium assembly / beta-catenin destruction complex / CRMPs in Sema3A signaling / heart valve development / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / tau-protein kinase / regulation of microtubule-based process / regulation of protein export from nucleus / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Maturation of nucleoprotein / cellular response to interleukin-3 / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / Maturation of nucleoprotein / tau-protein kinase activity / negative regulation of epithelial to mesenchymal transition / G protein-coupled dopamine receptor signaling pathway / positive regulation of cell-matrix adhesion / regulation of axonogenesis / regulation of dendrite morphogenesis / glycogen metabolic process / ER overload response / regulation of neuron projection development / establishment of cell polarity / protein kinase A catalytic subunit binding / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / epithelial to mesenchymal transition / Regulation of HSF1-mediated heat shock response / negative regulation of osteoblast differentiation / NF-kappaB binding / canonical Wnt signaling pathway / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / extrinsic apoptotic signaling pathway / cellular response to retinoic acid / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of autophagy / Transcriptional and post-translational regulation of MITF-M expression and activity / presynaptic modulation of chemical synaptic transmission / regulation of microtubule cytoskeleton organization / response to endoplasmic reticulum stress / negative regulation of cell migration / hippocampus development / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H2AS121 kinase activity / histone H3S57 kinase activity / excitatory postsynaptic potential / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H3S10 kinase activity / AMP-activated protein kinase activity / histone H3T11 kinase activity / histone H3T3 kinase activity / 3-phosphoinositide-dependent protein kinase activity / Ubiquitin-dependent degradation of Cyclin D / histone H3T45 kinase activity / mitochondrion organization / positive regulation of cell differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / positive regulation of protein-containing complex assembly / negative regulation of canonical Wnt signaling pathway / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2WE / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.711 Å
AuthorsLewis, H.A. / Sivaprakasam, P. / Kish, K. / Pokross, M. / Dubowchik, G.M.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Discovery of new acylaminopyridines as GSK-3 inhibitors by a structure guided in-depth exploration of chemical space around a pyrrolopyridinone core.
Authors: Sivaprakasam, P. / Han, X. / Civiello, R.L. / Jacutin-Porte, S. / Kish, K. / Pokross, M. / Lewis, H.A. / Ahmed, N. / Szapiel, N. / Newitt, J.A. / Baldwin, E.T. / Xiao, H. / Krause, C.M. / ...Authors: Sivaprakasam, P. / Han, X. / Civiello, R.L. / Jacutin-Porte, S. / Kish, K. / Pokross, M. / Lewis, H.A. / Ahmed, N. / Szapiel, N. / Newitt, J.A. / Baldwin, E.T. / Xiao, H. / Krause, C.M. / Park, H. / Nophsker, M. / Lippy, J.S. / Burton, C.R. / Langley, D.R. / Macor, J.E. / Dubowchik, G.M.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 2.0Feb 19, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen synthase kinase-3 beta
B: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2264
Polymers98,5902
Non-polymers6372
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-15 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.786, 81.894, 177.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycogen synthase kinase-3 beta / GSK-3 beta / Serine/threonine-protein kinase GSK3B


Mass: 49294.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-2WE / 2-[2-(cyclopropylcarbonylamino)pyridin-4-yl]-4-methoxy-1,3-thiazole-5-carboxamide


Mass: 318.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4
Details: GSK-3 was mixed with a 10-fold molar excess of 3 (1 mM final concentration). Crystals were grown at 20 C by vapor diffusion in the presence of 25% PEG 1500 and 0.1M MMT pH 4.0. Crystals ...Details: GSK-3 was mixed with a 10-fold molar excess of 3 (1 mM final concentration). Crystals were grown at 20 C by vapor diffusion in the presence of 25% PEG 1500 and 0.1M MMT pH 4.0. Crystals would nucleate within 1-3 days and continued to grow for an addition 5-10 days before harvesting, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.71→91.6292 Å / Num. obs: 32217

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.711→74.33 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2812 1628 5.07 %Random
Rwork0.2133 ---
obs0.2167 32079 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.711→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 42 45 4951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085046
X-RAY DIFFRACTIONf_angle_d1.1496929
X-RAY DIFFRACTIONf_dihedral_angle_d13.3051654
X-RAY DIFFRACTIONf_chiral_restr0.045769
X-RAY DIFFRACTIONf_plane_restr0.006930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7108-2.79060.42551220.30382415X-RAY DIFFRACTION96
2.7906-2.88060.32981490.28932460X-RAY DIFFRACTION99
2.8806-2.98360.34291180.26872538X-RAY DIFFRACTION100
2.9836-3.10310.31891400.26572489X-RAY DIFFRACTION100
3.1031-3.24430.36051390.25632510X-RAY DIFFRACTION100
3.2443-3.41530.32161390.23292511X-RAY DIFFRACTION100
3.4153-3.62930.29231510.222529X-RAY DIFFRACTION100
3.6293-3.90950.25081230.19992553X-RAY DIFFRACTION100
3.9095-4.30290.23821410.18012540X-RAY DIFFRACTION100
4.3029-4.92550.2731220.17622575X-RAY DIFFRACTION100
4.9255-6.20510.28631340.21532607X-RAY DIFFRACTION100
6.2051-74.35810.23021500.19362724X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1779-1.6179-1.22560.7225-0.04793.2163-0.6791-0.15710.5813-0.0436-0.2426-0.0430.4790.52870.46310.67550.0447-0.16830.21190.14620.75211.8623-12.6071-36.2306
23.2881-4.5736-2.10378.3091-0.67547.99450.42690.9637-1.0432-1.1089-0.58990.19331.0642-0.55320.4610.74310.2167-0.02220.3652-0.03980.60421.4581-18.6602-45.8254
31.3476-0.31371.70636.91294.91326.8684-0.3629-0.21760.99760.38860.1477-1.9768-0.43890.5166-0.30470.55760.057-0.02540.4116-0.14940.810211.5281-8.517-37.5957
44.00513.3667-0.66576.24224.51557.6464-1.0627-1.01560.51481.67830.21220.09950.8062-0.08670.83370.80840.086-0.16710.37670.04870.7189-2.2007-2.3233-27.4533
53.69141.22862.22881.2412-1.48377.2825-0.3785-1.0297-0.19150.52660.7732-0.14730.43090.1237-0.31930.5442-0.021-0.06340.2994-0.0310.81493.474-3.0321-32.0395
66.36833.7902-0.21984.9466-2.64732.82330.92020.45020.2849-0.78810.0972-0.41550.95791.1884-0.28990.72660.07120.20750.43840.08720.725911.6112-4.037-43.6581
79.69324.11352.3475.0702-0.9743.10140.0363-0.5362-0.43670.31120.50751.13521.1622-0.6704-0.440.7175-0.02640.23230.25970.10720.5825-3.3331-12.8656-32.6138
82.5745-2.68242.47383.6759-2.60172.37350.10450.0976-0.0868-0.4691-0.14190.17050.2995-0.01240.04180.7407-0.201-0.00690.3526-0.07430.4532-9.5304-10.6282-43.8525
96.4061-4.55044.77556.0588-2.96044.4079-0.0281.73840.7265-0.0761-0.2673-1.6981-0.1720.83160.5310.4403-0.00020.14610.445-0.0470.5677-2.3961-6.796-44.867
105.08110.10043.76111.8071-0.41714.83540.0951-1.3032-0.807-0.42770.0092-0.55430.2716-0.1719-0.27860.91270.1368-0.10710.49160.15970.59712.7381-15.3451-35.8396
112.7683-0.37520.01842.1381-0.63912.7448-0.5125-0.57580.05120.65930.479-0.08740.29220.15340.16650.61140.14050.10810.4473-0.05950.3329-0.4328-6.4117-34.8829
121.8687-0.63040.02250.28930.5724.1945-0.2278-0.27350.76470.98680.1108-0.8254-1.297-0.0622-0.04580.6505-0.0712-0.07740.3261-0.09230.5299-10.317517.3155-36.9129
130.6668-0.4351-0.9391.2211-0.43423.58930.03680.0011-0.19190.2575-0.04660.0530.3864-0.32190.00010.4997-0.10030.02310.3791-0.02550.3691-18.1176-1.1768-39.4302
141.8192-0.2451-0.02760.852-0.34381.39090.1487-0.2832-0.05960.2784-0.20660.0055-0.1394-0.2933-0.0220.37080.01390.02650.4299-0.0090.4043-25.38088.4118-33.3314
154.27371.65150.03296.3834-0.88316.68640.5130.1363-0.27780.2763-0.12861.2031-0.1045-2.2239-0.45220.6485-0.0379-0.06151.2004-0.10580.6485-38.53325.461-31.7533
162.06260.1817-0.48462.49780.39163.61850.01310.52370.1223-0.45370.1077-0.093-0.1508-0.7316-0.06010.5955-0.0606-0.0330.481-0.0440.4113-21.22686.6189-52.5846
175.90171.35580.80678.00920.77293.50150.11920.70620.695-0.3008-0.20290.2185-0.5376-0.31710.21790.23420.0227-0.14140.49520.26730.7105-35.290334.3578-9.1648
183.3413-1.4966-0.92211.76610.88050.4708-0.205-0.1128-0.06620.21060.09990.1941-0.058-0.5270.55830.36770.25780.31550.64190.10510.7995-43.946521.8641-0.1099
193.20951.78820.37127.7389-0.79772.2168-0.2845-0.00070.7580.0485-0.1009-0.0984-1.7939-0.2937-0.08220.6219-0.0347-0.00530.6674-0.04940.7107-33.432132.6716-6.3566
201.00530.7185-0.79490.7104-0.76210.8212-0.21.0436-0.5289-0.43970.313-0.44560.17960.29340.09070.32710.0880.20570.9180.03390.6767-25.683520.9769-17.7313
210.2521-1.0755-1.17035.21155.9487.24120.36060.82080.0395-0.16120.54230.46790.01670.08920.11260.3952-0.07050.05570.5721-0.11570.6379-27.260425.4788-12.5935
221.4190.18112.40012.6223-0.06337.91590.10150.6545-0.14110.38220.4879-0.6683-0.6507-0.2628-0.04640.3152-0.060.04180.4278-0.11080.4656-30.067326.6982-6.3624
231.52070.82080.26550.44210.14320.0460.5074-0.2003-0.3656-0.03870.20590.83190.161-0.48120.12270.17760.0064-0.0811.0323-0.06860.8166-44.041614.796-17.4597
242.887-0.9297-1.30773.51480.6561.46840.0894-0.61210.04910.11280.119-0.0833-0.0851-0.12040.20830.2362-0.1970.14820.7060.17460.2266-38.935711.7215-7.3208
257.8323-0.51523.05641.8025-2.74027.7273-0.7323-0.73090.40320.49630.20590.4585-0.2758-0.2108-0.13020.21530.16070.05250.6799-0.09990.4986-30.673610.54633.1717
263.9742-2.47930.72547.381-2.90753.00930.42340.1313-0.1460.03510.58960.4461-0.7743-0.151-0.02590.43290.14640.01220.55450.14740.4211-37.094721.4818-7.0645
271.9416-1.15930.56281.8939-0.9713.26230.0528-0.32380.24490.0324-0.184-0.2922-0.08610.08160.06110.373-0.10290.00910.3655-0.0420.4076-20.389310.7039-4.1129
286.59061.80090.68492.7989-1.24894.3655-0.24140.75070.29180.2330.33530.0403-0.2985-0.0153-0.09980.3717-0.06530.07850.4279-0.01040.4365-24.44319.7031-6.1151
293.23260.42420.23941.63561.06144.2795-0.04130.0533-0.5383-0.02840.0101-0.07881.1338-0.13130.04570.6431-0.0763-0.00150.4213-0.01460.4423-21.614-7.2466-15.4521
302.96911.7419-0.24873.35130.16593.5870.0288-0.2794-0.43260.5456-0.1631-0.50180.71210.67960.04570.6773-0.0363-0.01840.56010.08960.4795-16.041-5.1151.8224
313.36530.4273-2.68022.85850.16892.22220.3598-0.76760.18910.8566-0.0469-0.0555-0.0756-0.3487-0.24780.7767-0.146-0.03790.8660.07220.4236-24.53283.213812.7397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 59 )
4X-RAY DIFFRACTION4chain 'A' and (resid 60 through 67 )
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 74 )
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 80 )
7X-RAY DIFFRACTION7chain 'A' and (resid 81 through 95 )
8X-RAY DIFFRACTION8chain 'A' and (resid 96 through 108 )
9X-RAY DIFFRACTION9chain 'A' and (resid 109 through 113 )
10X-RAY DIFFRACTION10chain 'A' and (resid 114 through 119 )
11X-RAY DIFFRACTION11chain 'A' and (resid 124 through 138 )
12X-RAY DIFFRACTION12chain 'A' and (resid 139 through 154 )
13X-RAY DIFFRACTION13chain 'A' and (resid 155 through 235 )
14X-RAY DIFFRACTION14chain 'A' and (resid 236 through 273 )
15X-RAY DIFFRACTION15chain 'A' and (resid 274 through 304 )
16X-RAY DIFFRACTION16chain 'A' and (resid 305 through 381 )
17X-RAY DIFFRACTION17chain 'B' and (resid 35 through 42 )
18X-RAY DIFFRACTION18chain 'B' and (resid 43 through 51 )
19X-RAY DIFFRACTION19chain 'B' and (resid 52 through 59 )
20X-RAY DIFFRACTION20chain 'B' and (resid 60 through 67 )
21X-RAY DIFFRACTION21chain 'B' and (resid 68 through 74 )
22X-RAY DIFFRACTION22chain 'B' and (resid 75 through 87 )
23X-RAY DIFFRACTION23chain 'B' and (resid 88 through 95 )
24X-RAY DIFFRACTION24chain 'B' and (resid 96 through 103 )
25X-RAY DIFFRACTION25chain 'B' and (resid 104 through 108 )
26X-RAY DIFFRACTION26chain 'B' and (resid 109 through 119 )
27X-RAY DIFFRACTION27chain 'B' and (resid 124 through 175 )
28X-RAY DIFFRACTION28chain 'B' and (resid 176 through 203 )
29X-RAY DIFFRACTION29chain 'B' and (resid 204 through 304 )
30X-RAY DIFFRACTION30chain 'B' and (resid 305 through 349 )
31X-RAY DIFFRACTION31chain 'B' and (resid 350 through 385 )

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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